情节中缺少的部分，然后重新出现并在保存时覆盖整个情节？ （R，热图 2）
Parts Missing From Plot, That then Reappear and Overwrite The Entire Plot When Saved? (R, Heatmap.2)
我正在使用 heatmap.2 创建绘图，但是，保存到我的源文件夹中的初始绘图缺少密钥和标题。
当我再运行dev.off()命令时，Key和Title会被用来覆盖原来的图吗？
例如，我会制作这样一个情节：
这远非完美。但是当我 运行 dev.off() 关闭设备时（否则会出现许多其他错误）：
你在上面看到的是一个非常扭曲的Key和我的'XYZ'标题。
到底为什么要创建两个文件，第一个是我的矩阵，然后用第二个包含我的翻转键和我的标题的文件覆盖它？我跟不上逻辑。
我已经更新了我的 OS、我的 R、RStudio 版本、我所有的包和未安装的 RStudio。似乎没有任何帮助。
如果您想尝试复制我的错误，这里是示例矩阵：
structure(c(1, 4, 5, 3, 3, 4, 6, 1, 7, 5, 5, 4, 4, 8, 1, 3, 9,
2, 2, 9, 3, 1, 3, 4, 4, 5, 5, 5, 1, 4, 4, 3, 3, 3, 9, 1), .Dim = c(6L,
6L))
这是我用来绘制示例数据的脚本。您需要提供 SourceDir 并确保将矩阵分配给名称 "Matrix".
if (!require("gplots")) {
install.packages("gplots", dependencies = TRUE)
library(gplots)
}
if (!require("RColorBrewer")) {
install.packages("RColorBrewer", dependencies = TRUE)
library(RColorBrewer)
}
my_palette <- colorRampPalette(c("snow", "yellow", "darkorange", "red"))(n = 399)
transition
col_breaks = c(seq(0,1,length=100), #white 'snow'
seq(2,4,length=100), # for yellow
seq(5,7,length=100), # for orange 'darkorange'
seq(8,9,length=100)) # for red
png(paste(SourceDir, "Heatmap_Test.png"),
width = 5*1000,
height = 5*1000,
res = 300,
pointsize =15)
heatmap.2(Matrix,
main = paste("XYZ"),
notecol="black",
key = "true" ,
colsep = c(3, 6, 9),
rowsep = c(3, 6, 9),
labCol = NULL,
labRow = NULL,
sepcolor="white",
sepwidth=c(0.08,0.08),
density.info="none",
trace="none",
margins=c(1,1),
col=my_palette,
breaks=col_breaks,
dendrogram="none",
RowSideColors = c(rep("blue", 3), rep("orange", 3)),
ColSideColors = c(rep("blue", 3), rep("orange", 3)),
srtCol = 0 ,
asp = 1 ,
adjCol = c(NA, 0) ,
adjRow = c(0, NA) ,
#keysize = 2 ,
Colv = FALSE ,
Rowv = FALSE ,
key.xlab = paste("Correlation") ,
cexRow = (1.8) ,
cexCol = (1.8) ,
notecex = (1.5) ,
lmat = rbind(c(0,0,0,0), c(0,0,2,0),c(0,1,3,0),c(0,0,0,0)) ,
#par(ColSideColors = c(2,2)),
lhei = c(1, 1, 3, 1) ,
lwid = c(1, 1, 3, 1))
dev.off()
如果能深入了解这个问题，我将不胜感激。
我认为这是因为我拥有的不仅仅是元素 1 到 4，因为我添加的彩色行算作必须在显示矩阵中排列的附加元素。
因此：
mat = rbind(c(0,0,0,0), c(0,0,2,0),c(0,1,3,0),c(0,0,0,0)) ,
lhei = c(1, 1, 3, 1) ,
lwid = c(1, 1, 3, 1))
不再切黄油。费了九牛二虎之力，我终于设法让下面的布局工作（在我的实际数据上，而不是我的示例数据上）。
lmat = rbind(c(0,4,5,0), c(0,0,2,0),c(0,1,3,0),c(0,0,6,0)) ,
lhei = c(0.4, 0.16, 3, 0.4) , # Alter dimensions of display array cell heighs
lwid = c(0.4, 0.16, 3, 0.4),
注意包含元素 5 和 6。
所以我的最终命令看起来像这样（请注意，还会有许多其他更改，但真正的进展发生在我添加 5 和 6 之后）：
png(paste(SourceDir, "XYZ.png"),
width = 5*1500,
height = 5*1500,
res = 300, # 300 pixels per inch
pointsize =30)
heatmap.2(CombinedMtx,
main = paste("XYZ"), # heat map title
notecol="black",
key = "true" ,# change font color of cell labels to black
colsep = c(6, 12, 18),
labCol = c(" "," "," ", "XX"," "," "," "," "," ", "YY"," "," "," "," "," ", "ZZ"," "," "," "," "," ", "QQ"),
rowsep = c(6, 12, 18),
labRow = c(" "," "," ", "XX"," "," "," "," "," ", "YY"," "," "," "," "," ", "ZZ"," "," "," "," "," ", "QQ"),
sepcolor="white",
sepwidth=c(0.08,0.08),
density.info="none",
trace="none",
margins=c(1,1),
col=my_palette,
breaks=col_breaks,
dendrogram="none",
RowSideColors = c(rep("#deebf7", 6), rep("#1c9099", 6), rep("#addd8e", 6), rep("#fee391", 6)),
ColSideColors = c(rep("#deebf7", 6), rep("#1c9099", 6), rep("#addd8e", 6), rep("#fee391", 6)),
srtCol = 0 ,
asp = 1 ,
adjCol = c(1.5, -61.5) ,
adjRow = c(0, -1.38),
offsetRow = (-59.5),
keysize = 2 ,
Colv = FALSE ,
Rowv = FALSE ,
key.xlab = NA ,
key.ylab = NULL ,
key.title = NA ,
cexRow = (1.6) ,
cexCol = (1.6) ,
notecex = (1.5) ,
cex.main = (20),
lmat = rbind(c(0,4,5,0), c(0,0,2,0),c(0,1,3,0),c(0,0,6,0)) ,
#par(ColSideColors = c(2,2)),
lhei = c(0.4, 0.16, 3, 0.4) , # Alter dimensions of display array cell heighs
lwid = c(0.4, 0.16, 3, 0.4),
symkey = any(0.5 < 0, na.rm=FALSE) || col_breaks,
key.par=list(mar=c(3.5,0, 1.8,0) ) #tweak specific key paramters
)
dev.off()
此外，如果您不是每次都通过使用 dev.off() 创建 PNG 和 enf 开始，它将无法工作。我相信这也可能导致我的困惑，并且可能在绘制热图之后，一旦 dev.off() 命令为 运行，就会绘制一些元素，导致热图被覆盖。
这（用我的矩阵）创建了这个图像。
我所做的是一种非常巧妙的方法来标记我的块，但在我弄清楚如何让 ComplexHeatmap 正常工作之前，我将被困在 Heatmap.2 中使用这样的技巧。
我正在使用 heatmap.2 创建绘图，但是，保存到我的源文件夹中的初始绘图缺少密钥和标题。
当我再运行dev.off()命令时，Key和Title会被用来覆盖原来的图吗？
例如，我会制作这样一个情节：
这远非完美。但是当我 运行 dev.off() 关闭设备时（否则会出现许多其他错误）：
你在上面看到的是一个非常扭曲的Key和我的'XYZ'标题。
到底为什么要创建两个文件，第一个是我的矩阵，然后用第二个包含我的翻转键和我的标题的文件覆盖它？我跟不上逻辑。
我已经更新了我的 OS、我的 R、RStudio 版本、我所有的包和未安装的 RStudio。似乎没有任何帮助。
如果您想尝试复制我的错误，这里是示例矩阵：
structure(c(1, 4, 5, 3, 3, 4, 6, 1, 7, 5, 5, 4, 4, 8, 1, 3, 9,
2, 2, 9, 3, 1, 3, 4, 4, 5, 5, 5, 1, 4, 4, 3, 3, 3, 9, 1), .Dim = c(6L,
6L))
这是我用来绘制示例数据的脚本。您需要提供 SourceDir 并确保将矩阵分配给名称 "Matrix".
if (!require("gplots")) {
install.packages("gplots", dependencies = TRUE)
library(gplots)
}
if (!require("RColorBrewer")) {
install.packages("RColorBrewer", dependencies = TRUE)
library(RColorBrewer)
}
my_palette <- colorRampPalette(c("snow", "yellow", "darkorange", "red"))(n = 399)
transition
col_breaks = c(seq(0,1,length=100), #white 'snow'
seq(2,4,length=100), # for yellow
seq(5,7,length=100), # for orange 'darkorange'
seq(8,9,length=100)) # for red
png(paste(SourceDir, "Heatmap_Test.png"),
width = 5*1000,
height = 5*1000,
res = 300,
pointsize =15)
heatmap.2(Matrix,
main = paste("XYZ"),
notecol="black",
key = "true" ,
colsep = c(3, 6, 9),
rowsep = c(3, 6, 9),
labCol = NULL,
labRow = NULL,
sepcolor="white",
sepwidth=c(0.08,0.08),
density.info="none",
trace="none",
margins=c(1,1),
col=my_palette,
breaks=col_breaks,
dendrogram="none",
RowSideColors = c(rep("blue", 3), rep("orange", 3)),
ColSideColors = c(rep("blue", 3), rep("orange", 3)),
srtCol = 0 ,
asp = 1 ,
adjCol = c(NA, 0) ,
adjRow = c(0, NA) ,
#keysize = 2 ,
Colv = FALSE ,
Rowv = FALSE ,
key.xlab = paste("Correlation") ,
cexRow = (1.8) ,
cexCol = (1.8) ,
notecex = (1.5) ,
lmat = rbind(c(0,0,0,0), c(0,0,2,0),c(0,1,3,0),c(0,0,0,0)) ,
#par(ColSideColors = c(2,2)),
lhei = c(1, 1, 3, 1) ,
lwid = c(1, 1, 3, 1))
dev.off()
如果能深入了解这个问题，我将不胜感激。
我认为这是因为我拥有的不仅仅是元素 1 到 4，因为我添加的彩色行算作必须在显示矩阵中排列的附加元素。
因此：
mat = rbind(c(0,0,0,0), c(0,0,2,0),c(0,1,3,0),c(0,0,0,0)) ,
lhei = c(1, 1, 3, 1) ,
lwid = c(1, 1, 3, 1))
不再切黄油。费了九牛二虎之力，我终于设法让下面的布局工作（在我的实际数据上，而不是我的示例数据上）。
lmat = rbind(c(0,4,5,0), c(0,0,2,0),c(0,1,3,0),c(0,0,6,0)) ,
lhei = c(0.4, 0.16, 3, 0.4) , # Alter dimensions of display array cell heighs
lwid = c(0.4, 0.16, 3, 0.4),
注意包含元素 5 和 6。
所以我的最终命令看起来像这样（请注意，还会有许多其他更改，但真正的进展发生在我添加 5 和 6 之后）：
png(paste(SourceDir, "XYZ.png"),
width = 5*1500,
height = 5*1500,
res = 300, # 300 pixels per inch
pointsize =30)
heatmap.2(CombinedMtx,
main = paste("XYZ"), # heat map title
notecol="black",
key = "true" ,# change font color of cell labels to black
colsep = c(6, 12, 18),
labCol = c(" "," "," ", "XX"," "," "," "," "," ", "YY"," "," "," "," "," ", "ZZ"," "," "," "," "," ", "QQ"),
rowsep = c(6, 12, 18),
labRow = c(" "," "," ", "XX"," "," "," "," "," ", "YY"," "," "," "," "," ", "ZZ"," "," "," "," "," ", "QQ"),
sepcolor="white",
sepwidth=c(0.08,0.08),
density.info="none",
trace="none",
margins=c(1,1),
col=my_palette,
breaks=col_breaks,
dendrogram="none",
RowSideColors = c(rep("#deebf7", 6), rep("#1c9099", 6), rep("#addd8e", 6), rep("#fee391", 6)),
ColSideColors = c(rep("#deebf7", 6), rep("#1c9099", 6), rep("#addd8e", 6), rep("#fee391", 6)),
srtCol = 0 ,
asp = 1 ,
adjCol = c(1.5, -61.5) ,
adjRow = c(0, -1.38),
offsetRow = (-59.5),
keysize = 2 ,
Colv = FALSE ,
Rowv = FALSE ,
key.xlab = NA ,
key.ylab = NULL ,
key.title = NA ,
cexRow = (1.6) ,
cexCol = (1.6) ,
notecex = (1.5) ,
cex.main = (20),
lmat = rbind(c(0,4,5,0), c(0,0,2,0),c(0,1,3,0),c(0,0,6,0)) ,
#par(ColSideColors = c(2,2)),
lhei = c(0.4, 0.16, 3, 0.4) , # Alter dimensions of display array cell heighs
lwid = c(0.4, 0.16, 3, 0.4),
symkey = any(0.5 < 0, na.rm=FALSE) || col_breaks,
key.par=list(mar=c(3.5,0, 1.8,0) ) #tweak specific key paramters
)
dev.off()
此外，如果您不是每次都通过使用 dev.off() 创建 PNG 和 enf 开始，它将无法工作。我相信这也可能导致我的困惑，并且可能在绘制热图之后，一旦 dev.off() 命令为 运行，就会绘制一些元素，导致热图被覆盖。
这（用我的矩阵）创建了这个图像。
我所做的是一种非常巧妙的方法来标记我的块，但在我弄清楚如何让 ComplexHeatmap 正常工作之前，我将被困在 Heatmap.2 中使用这样的技巧。